Species validation and cryptic diversity in the Geophagus brasiliensis Quoy &amp; Gaimard, 1824 complex (Teleostei, Cichlidae) from Brazilian coastal basins as revealed by DNA analyses

Souza, Cássio Ribeiro; Affonso, Paulo Roberto Antunes de Mello; Bitencourt, Jamille de Araújo; Sampaio, Iracilda; Carneiro, Paulo Luız Souza

doi:10.1007/s10750-017-3482-y

Cited by 15 publications

(13 citation statements)

References 49 publications

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“…Due to the extensive sampling, discovering cryptic species within the scope of population genetic studies is not a rare phenomenon 1–3 . Traditionally, cryptic species/diversity in fishes is mostly discovered in highly variable taxa, especially in the species rich lineages of ray-finned fishes, such as the neotropical Characidae 4,5 or Cichlidae 6,7 . Cryptic diversity was also found - albeit less frequently - in other lineages, e.g.…”

Section: Introductionmentioning

confidence: 99%

From taxonomic deflation to newly detected cryptic species: Hidden diversity in a widespread African squeaker catfish

Jírsová

Štefka

Blažek

et al. 2019

Sci Rep

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Cryptic genetic diversity and erroneous morphological species determination represent frequent problems in biodiversity research. Here, examination of 138 specimens of Synodontis (Mochokidae, Siluriformes) from the Nile River and Lake Turkana revealed the presence of both S. schall-like and S. frontosus-like morphotypes, with a phenotypic gradient between them. We concluded phylogenetic and population genetic analyses based on two mitochondrial and one nuclear marker including 131 coxI (565 bp), 96 cytb (973 bp) and 19 RAG2 (896 bp) sequences from the Nile-Turkana population, plus additional GenBank data of Synodontis spp. Whilst nuclear data were inconclusive, mitochondrial sequences suggested that both morphotypes and intermediate forms are conspecific. The results imply probable synonymy of S. frontosus with S. schall. Conversely, a strong biogeographical signal was revealed among widely distributed and supposedly conspecific S. schall-like catfish of the Nilo-Sudanian ichthyological province. Synodontis schall sensu stricto (=Eastern clade), as defined by type locality in the Nile, is apparently restricted to the eastern part of the Nilo-Sudanian ichthyological province (e.g. Nile, Turkana, Chad). Synodontis schall Western clade (Senegambia, Niger, Chad) most probably represents a cryptic taxon, unrecognized thus far due to the absence of distinctive morphological differences.

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Section: Introductionmentioning

confidence: 99%

From taxonomic deflation to newly detected cryptic species: Hidden diversity in a widespread African squeaker catfish

Jírsová

Štefka

Blažek

et al. 2019

Sci Rep

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“…The biological significance of this variation has yet to be investigated, and it is currently unclear whether these morphological differences represent intraspecific variation or potentially indicate the existence of multiple species. The combination of phenotypic and molecular data in an integrative approach has been used as an efficient tool in fish population studies, and its use has contributed to the identification of cryptic species (Fagundes et al, 2020; Nascimento et al, 2023; Prizon et al, 2017; Souza et al, 2018). This research therefore performs an integrative taxonomy comparison between populations of Otocinclus cocama in the Ucayali and Tigre (Maranõn drainage) river basins, applying geometric morphometric approaches and DNA sequences of four mitochondrial genes to assess the existence of undetected cryptic species diversity or con‐specificity across different geographic areas.…”

Section: Introductionmentioning

confidence: 99%

Molecular and morphometric data provide evidence of intraspecific variation in shape and pigmentation pattern in Otocinclus cocama (Siluriformes: Loricariidae) across major river drainages

Mejia,

Reis

2023

Journal of Fish Biology

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Otocinclus cocama, a uniquely colored species of the loricariid catfish genus Otocinclus described solely from the type locality in the lower Ucayali River in northern Peru, is reported occurring in the Tigre River, a tributary to the Marañón River that drains a different section of the Andean Mountain range in the western Amazon. Both populations differ in the number of dark bars spanning the flanks of the body, and we investigated whether these morphotypes constitute distinct species. The body shapes of populations from the Tigre and Ucayali rivers were compared using geometric morphometrics. Although principal component analysis detected a broad overlap between populations, multivariate analysis of variance and linear driscriminat analysis revealed a subtle differentiation between the populations of the two hydrographic basins. Average body shape of the Ucayali River population tend to be slightly higher than that of the Tigre River, with the caudal peduncle stretched vertically in the Ucayali population. Multivariate regression of shape and centroid size revealed an allometric effect of 10.7% (p < 0.001), suggesting that the variation between Tigre and Ucayali populations was purely shape variation. Molecular data of coI, cytb, nd2, and 16S mitochondrial genes indicated a nucleotide diversity range from 0.001 to 0.003, and haplotypic diversity range from 0.600 ± 0.11 to 0.79 ± 0.07. The median‐joining haplotype network for the concatenated matrix exhibited two divergent haplogroups related to the geographic area and separated by <10 mutational steps. The molecular species delimitation methods based on distance (automatic barcode gap discovery and assemble species by automatic partitioning) recovered two molecular lineages evolving independently, being one of the lineages formed by individuals from both populations. Tree‐based methods (generalized mixed Yule coalescent and Bayesian implementation of the Poisson tree process) recovered similar topologies and supported single lineage recognition. Methods of molecular delimitation of species disclosed the high similarity between the two populations of Otocinclus cocama, further supported by the presence of old haplotypes common to both groups which could indicate that the populations still maintain gene flow. Although the morphological data reveal a subtle variation between both river basins, the molecular data suggest a weak population structuration based on hydrographic areas, but not different species lineages, therefore Otocinclus cocama is composed of a single lineage with two distinct morphotypes.

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“…Sequences of the mitochondrial DNA gene cytochrome c oxidase (COI) are often used to assist taxonomy and species identification following the DNA barcoding principles ( Hebert, Ratnasingham & DeWaard, 2003 ; Hajibabaei et al, 2007 ). They can also be used for biodiversity inventories ( Monaghan et al, 2009 ; Carvalho et al, 2011 ; Pereira et al, 2013 ; Machado et al, 2018 ), allowing rapid characterization of not just a given sample but of entire communities ( Carvalho et al, 2018 ; Machado et al, 2018 ; Souza et al, 2018 ; Arruda et al, 2019 ; Santos et al, 2019 ). The simplest approach to delimit species from DNA sequence data is to use the percent cut-off rule ( Fujisawa & Barraclough, 2013 ), such as the 2% intra vs .…”

Section: Introductionmentioning

confidence: 99%

Mapping the hidden diversity of the Geophagus sensu stricto species group (Cichlidae: Geophagini) from the Amazon basin

Ximenes

Bittencourt

Machado

et al. 2021

PeerJ

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South American freshwater ichthyofauna is taxonomically the most diverse on the planet, yet its diversity is still vastly underestimated. The Amazon basin alone holds more than half of this diversity. The evidence of this underestimation comes from the backlog of morphologically distinct, yet undescribed forms deposited in museum collections, and from DNA-based inventories which consistently identify large numbers of divergent lineages within even well-studied species groups. In the present study, we investigated lineage diversity within the Geophagus sensu stricto species group. To achieve these objectives, we analyzed 337 individuals sampled from 77 locations within and outside the Amazon basin representing 10 nominal and six morphologically distinct but undescribed species. We sequenced the mitochondrial cytochrome c oxidase subunit I (COI) and delimited lineages using four different single-locus species discovery methods (mPTP-15 lineages; LocMin-14 lineages; bGMYC-18 lineages; and GMYC-30 lineages). The six morphologically distinct but undescribed species were also delimited by the majority of the species discovery methods. Five of these lineages are restricted to a single collection site or a watershed and their habitats are threatened by human activities such as deforestation, agricultural activities and construction of hydroelectric plants. Our results also highlight the importance of combining DNA and morphological data in biodiversity assessment studies especially in taxonomically diverse tropical biotas.

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Species validation and cryptic diversity in the Geophagus brasiliensis Quoy & Gaimard, 1824 complex (Teleostei, Cichlidae) from Brazilian coastal basins as revealed by DNA analyses

Cited by 15 publications

References 49 publications

From taxonomic deflation to newly detected cryptic species: Hidden diversity in a widespread African squeaker catfish

From taxonomic deflation to newly detected cryptic species: Hidden diversity in a widespread African squeaker catfish

Molecular and morphometric data provide evidence of intraspecific variation in shape and pigmentation pattern in Otocinclus cocama (Siluriformes: Loricariidae) across major river drainages

Mapping the hidden diversity of the Geophagus sensu stricto species group (Cichlidae: Geophagini) from the Amazon basin

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